Starting phenix.real_space_refine
on Tue Mar  3 18:24:46 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7n4x_24180/03_2026/7n4x_24180.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n4x_24180/03_2026/7n4x_24180.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n4x_24180/03_2026/7n4x_24180.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n4x_24180/03_2026/7n4x_24180.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n4x_24180/03_2026/7n4x_24180.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n4x_24180/03_2026/7n4x_24180.map"
  }
  resolution = 3.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    4992      2.51       5
     N    1218      2.21       5
     O    1392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7647
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 953, 7423
          Classifications: {'peptide': 953}
          Link IDs: {'PTRANS': 50, 'TRANS': 902}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 140
          Unusual residues: {'CLR': 3, 'NAG': 4}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.57, per 1000 atoms: 0.21
  Number of scatterers: 7647
  At special positions: 0
  Unit cell: (134.113, 93.296, 79.135, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1392      8.00
     N    1218      7.00
     C    4992      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 471 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 525 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 920 " - pdb=" SG  CYS A 925 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 966 " - pdb=" SG  CYS A1024 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 967 " - pdb=" SG  CYS A 993 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 980 " - pdb=" SG  CYS A 989 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM 7561  O5  NAG A1404 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A1401 " - " ASN A 431 "
      " NAG A1402 " - " ASN A 464 "
      " NAG A1403 " - " ASN A 506 "
      " NAG A1404 " - " ASN A1075 "
      " NAG B   1 " - " ASN A 497 "
      " NAG C   1 " - " ASN A 909 "
      " NAG D   1 " - " ASN A1037 "
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 308.9 milliseconds
  

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1790

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 8 sheets defined
      61.8% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 333 through 351
      removed outlier: 3.594A  pdb=" N   TRP A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 368
      removed outlier: 3.563A  pdb=" N   ILE A 355 " --> pdb=" O   TRP A 351 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 378 through 384
      removed outlier: 3.575A  pdb=" N   LEU A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 401
    Processing helix  chain 'A' and resid 437 through 453
      removed outlier: 3.540A  pdb=" N   LEU A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   HIS A 453 " --> pdb=" O   GLU A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 481 through 485
      removed outlier: 4.004A  pdb=" N   CYS A 485 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 493
      No H-bonds generated for 'chain 'A' and resid 491 through 493'
    Processing helix  chain 'A' and resid 497 through 502
    Processing helix  chain 'A' and resid 517 through 528
      removed outlier: 3.953A  pdb=" N   HIS A 521 " --> pdb=" O   ASP A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 555
      removed outlier: 3.666A  pdb=" N   ALA A 555 " --> pdb=" O   PHE A 551 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 551 through 555'
    Processing helix  chain 'A' and resid 563 through 567
    Processing helix  chain 'A' and resid 585 through 607
    Processing helix  chain 'A' and resid 619 through 630
      removed outlier: 3.618A  pdb=" N   ASN A 626 " --> pdb=" O   GLU A 622 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   THR A 628 " --> pdb=" O   GLU A 624 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ALA A 630 " --> pdb=" O   ASN A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 649
      removed outlier: 3.903A  pdb=" N   SER A 639 " --> pdb=" O   ILE A 635 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR A 640 " --> pdb=" O   PHE A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 664
    Processing helix  chain 'A' and resid 665 through 690
      removed outlier: 3.787A  pdb=" N   LEU A 690 " --> pdb=" O   PHE A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 724
      removed outlier: 4.671A  pdb=" N   ASP A 712 " --> pdb=" O   SER A 708 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ASN A 713 " --> pdb=" O   VAL A 709 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ILE A 714 " --> pdb=" O   GLY A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 762
      Proline residue:  A 745  - end of helix
    Processing helix  chain 'A' and resid 766 through 804
      removed outlier: 3.563A  pdb=" N   SER A 789 " --> pdb=" O   LEU A 785 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   PHE A 791 " --> pdb=" O   GLN A 787 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   VAL A 792 " --> pdb=" O   MET A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 835
    Processing helix  chain 'A' and resid 835 through 841
      removed outlier: 3.670A  pdb=" N   PHE A 839 " --> pdb=" O   ALA A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 864
      removed outlier: 3.922A  pdb=" N   ARG A 846 " --> pdb=" O   HIS A 842 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   GLY A 847 " --> pdb=" O   TRP A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 881 through 893
      removed outlier: 4.370A  pdb=" N   ASP A 885 " --> pdb=" O   SER A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 918
      removed outlier: 3.892A  pdb=" N   ALA A 918 " --> pdb=" O   ALA A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 939
    Processing helix  chain 'A' and resid 952 through 961
    Processing helix  chain 'A' and resid 1004 through 1017
      Proline residue:  A1013  - end of helix
      removed outlier: 3.548A  pdb=" N   ASN A1017 " --> pdb=" O   PRO A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1081
      removed outlier: 3.549A  pdb=" N   ASP A1079 " --> pdb=" O   ASN A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1103 through 1107
    Processing helix  chain 'A' and resid 1108 through 1130
      Proline residue:  A1122  - end of helix
    Processing helix  chain 'A' and resid 1134 through 1160
    Processing helix  chain 'A' and resid 1164 through 1178
    Processing helix  chain 'A' and resid 1178 through 1191
      removed outlier: 4.442A  pdb=" N   HIS A1184 " --> pdb=" O   GLU A1180 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ILE A1185 " --> pdb=" O   PHE A1181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1196 through 1225
      removed outlier: 4.195A  pdb=" N   MET A1218 " --> pdb=" O   ALA A1214 " (cutoff:3.500A)
      Proline residue:  A1222  - end of helix
    Processing helix  chain 'A' and resid 1226 through 1230
    Processing helix  chain 'A' and resid 1232 through 1239
    Processing helix  chain 'A' and resid 1240 through 1254
    Processing helix  chain 'A' and resid 1256 through 1266
      removed outlier: 3.927A  pdb=" N   VAL A1260 " --> pdb=" O   VAL A1256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1270 through 1276
      removed outlier: 3.780A  pdb=" N   ALA A1274 " --> pdb=" O   ASN A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1282
      removed outlier: 3.623A  pdb=" N   GLU A1282 " --> pdb=" O   LYS A1278 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 489
    Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 489
      removed outlier: 3.538A  pdb=" N   VAL A 410 " --> pdb=" O   MET A 572 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 420 through 423
    Processing sheet with id=AA4, first strand: chain 'A' and resid 456 through 457
    Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 509
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1050 through 1052
    Processing sheet with id=AA7, first strand: chain 'A' and resid 979 through 980
      removed outlier: 3.772A  pdb=" N   ARG A 968 " --> pdb=" O   CYS A 980 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LYS A 991 " --> pdb=" O   LEU A 969 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1036 through 1038
      removed outlier: 7.179A  pdb=" N   ASN A1037 " --> pdb=" O   LEU A1045 " (cutoff:3.500A)

    414 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 0.98 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1372
        1.33 -     1.45: 1956
        1.45 -     1.58: 4441
        1.58 -     1.70: 0
        1.70 -     1.82: 69
  Bond restraints: 7838
  Sorted by residual:
  bond pdb=" N   ILE A 470 "
       pdb=" CA  ILE A 470 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.042 9.50e-03 1.11e+04 1.98e+01
  bond pdb=" N   TYR A 579 "
       pdb=" CA  TYR A 579 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 8.30e-03 1.45e+04 1.68e+01
  bond pdb=" N   LEU A 818 "
       pdb=" CA  LEU A 818 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.036 8.70e-03 1.32e+04 1.67e+01
  bond pdb=" N   LEU A1109 "
       pdb=" CA  LEU A1109 "
    ideal  model  delta    sigma   weight residual
    1.463  1.491 -0.028 6.90e-03 2.10e+04 1.63e+01
  bond pdb=" N   LEU A1221 "
       pdb=" CA  LEU A1221 "
    ideal  model  delta    sigma   weight residual
    1.462  1.493 -0.032 8.50e-03 1.38e+04 1.38e+01
  ... (remaining 7833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 6814
        1.54 -     3.08: 2982
        3.08 -     4.62: 779
        4.62 -     6.16: 111
        6.16 -     7.70: 6
  Bond angle restraints: 10692
  Sorted by residual:
  angle pdb=" N   VAL A 813 "
        pdb=" CA  VAL A 813 "
        pdb=" C   VAL A 813 "
      ideal   model   delta    sigma   weight residual
     113.10  108.53    4.57 9.70e-01 1.06e+00 2.22e+01
  angle pdb=" C   ARG A 846 "
        pdb=" N   GLY A 847 "
        pdb=" CA  GLY A 847 "
      ideal   model   delta    sigma   weight residual
     119.94  124.95   -5.01 1.11e+00 8.12e-01 2.03e+01
  angle pdb=" C   MET A 684 "
        pdb=" N   GLY A 685 "
        pdb=" CA  GLY A 685 "
      ideal   model   delta    sigma   weight residual
     119.94  124.94   -5.00 1.11e+00 8.12e-01 2.03e+01
  angle pdb=" C   SER A1137 "
        pdb=" N   GLY A1138 "
        pdb=" CA  GLY A1138 "
      ideal   model   delta    sigma   weight residual
     119.98  124.91   -4.93 1.11e+00 8.12e-01 1.97e+01
  angle pdb=" N   ARG A1279 "
        pdb=" CA  ARG A1279 "
        pdb=" C   ARG A1279 "
      ideal   model   delta    sigma   weight residual
     113.28  107.87    5.41 1.22e+00 6.72e-01 1.97e+01
  ... (remaining 10687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.73: 4641
       24.73 -    49.47: 245
       49.47 -    74.20: 25
       74.20 -    98.93: 15
       98.93 -   123.66: 4
  Dihedral angle restraints: 4930
    sinusoidal: 2154
      harmonic: 2776
  Sorted by residual:
  dihedral pdb=" CB  CYS A 525 "
           pdb=" SG  CYS A 525 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.22  -65.22     1      1.00e+01 1.00e-02 5.58e+01
  dihedral pdb=" CA  PRO A 815 "
           pdb=" C   PRO A 815 "
           pdb=" N   GLN A 816 "
           pdb=" CA  GLN A 816 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.33  -25.67     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CB  CYS A 980 "
           pdb=" SG  CYS A 980 "
           pdb=" SG  CYS A 989 "
           pdb=" CB  CYS A 989 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.79   39.21     1      1.00e+01 1.00e-02 2.16e+01
  ... (remaining 4927 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.938: 1269
       0.938 -    1.875: 2
       1.875 -    2.813: 1
       2.813 -    3.750: 0
       3.750 -    4.688: 2
  Chirality restraints: 1274
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    2.29   -4.69 2.00e-02 2.50e+03 5.49e+04
  chirality pdb=" C1  NAG A1404 "
            pdb=" ND2 ASN A1075 "
            pdb=" C2  NAG A1404 "
            pdb=" O5  NAG A1404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    1.70   -4.10 2.00e-01 2.50e+01 4.21e+02
  chirality pdb=" C1  NAG A1403 "
            pdb=" ND2 ASN A 506 "
            pdb=" C2  NAG A1403 "
            pdb=" O5  NAG A1403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.48   -1.92 2.00e-01 2.50e+01 9.20e+01
  ... (remaining 1271 not shown)

  Planarity restraints: 1328
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "    0.247 2.00e-02 2.50e+03   2.05e-01 5.28e+02
        pdb=" C7  NAG B   1 "   -0.066 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "    0.171 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "   -0.341 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 431 "   -0.115 2.00e-02 2.50e+03   1.88e-01 4.41e+02
        pdb=" CG  ASN A 431 "    0.054 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 431 "   -0.068 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 431 "    0.336 2.00e-02 2.50e+03
        pdb=" C1  NAG A1401 "   -0.207 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 909 "   -0.149 2.00e-02 2.50e+03   1.66e-01 3.45e+02
        pdb=" CG  ASN A 909 "    0.066 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 909 "    0.020 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 909 "    0.265 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.202 2.00e-02 2.50e+03
  ... (remaining 1325 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 124
        2.69 -     3.24: 7080
        3.24 -     3.79: 11687
        3.79 -     4.35: 15572
        4.35 -     4.90: 27215
  Nonbonded interactions: 61678
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 912 "
            pdb=" O5  NAG C   1 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OG  SER A 912 "
            pdb=" O6  NAG C   1 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   VAL A 380 "
            pdb=" OG  SER A 384 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   GLY A 710 "
            pdb=" NE2 GLN A 787 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" O   THR A 629 "
            pdb=" NE2 GLN A 700 "
     model   vdw
     2.384 3.120
  ... (remaining 61673 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.120
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.111   7854  Z= 1.068
  Angle     :  1.914  40.299  10734  Z= 1.343
  Chirality :  0.211   4.688   1274
  Planarity :  0.009   0.205   1321
  Dihedral  : 15.861 123.663   3122
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  7.40 %
    Favored  : 91.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.23), residues: 951
  helix: -1.73 (0.18), residues: 516
  sheet: -2.85 (0.54), residues: 62
  loop : -2.28 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 606 
 TYR   0.025   0.002   TYR A 646 
 PHE   0.039   0.003   PHE A 791 
 TRP   0.016   0.002   TRP A 960 
 HIS   0.007   0.002   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.01389 ( 7838)
  covalent geometry    : angle       1.76280 (10692)
  SS BOND              : bond        0.00404 (    6)
  SS BOND              : angle       1.21169 (   12)
  hydrogen bonds       : bond        0.15939 (  412)
  hydrogen bonds       : angle       6.71126 ( 1188)
  link_BETA1-4         : bond        0.00017 (    3)
  link_BETA1-4         : angle       0.48376 (    9)
  link_NAG-ASN         : bond        0.05685 (    7)
  link_NAG-ASN         : angle      17.00929 (   21)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A  351 TRP cc_start: 0.6880 (m100) cc_final: 0.6438 (m-10)
REVERT: A  483 TYR cc_start: 0.7814 (m-80) cc_final: 0.7557 (m-80)
REVERT: A  610 MET cc_start: 0.7717 (ttm) cc_final: 0.7166 (ttm)
REVERT: A  657 TRP cc_start: 0.6469 (OUTLIER) cc_final: 0.5110 (t60)
REVERT: A  943 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7224 (mt0)
REVERT: A 1091 GLU cc_start: 0.7135 (tt0) cc_final: 0.6889 (tt0)
REVERT: A 1218 MET cc_start: 0.7734 (mmt) cc_final: 0.7510 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 109
  average time/residue: 0.0723
  time to fit residues: 11.3923
Evaluate side-chains
  77 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  920 CYS
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1255 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0030
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 339 GLN
A 397 HIS
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1253 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.125911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.101990 restraints weight = 9118.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.47
r_work: 0.2943 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7854  Z= 0.146
  Angle     :  0.732  14.625  10734  Z= 0.329
  Chirality :  0.044   0.345   1274
  Planarity :  0.004   0.033   1321
  Dihedral  :  9.445  81.005   1442
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.42 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  9.37 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.27), residues: 951
  helix:  0.12 (0.22), residues: 550
  sheet: -1.86 (0.57), residues: 63
  loop : -1.65 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 693 
 TYR   0.014   0.001   TYR A 886 
 PHE   0.016   0.001   PHE A 791 
 TRP   0.013   0.001   TRP A 960 
 HIS   0.005   0.001   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7838)
  covalent geometry    : angle       0.66488 (10692)
  SS BOND              : bond        0.00300 (    6)
  SS BOND              : angle       0.99223 (   12)
  hydrogen bonds       : bond        0.04592 (  412)
  hydrogen bonds       : angle       4.56710 ( 1188)
  link_BETA1-4         : bond        0.00853 (    3)
  link_BETA1-4         : angle       2.49244 (    9)
  link_NAG-ASN         : bond        0.00398 (    7)
  link_NAG-ASN         : angle       6.77447 (   21)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7584 (m100) cc_final: 0.7297 (m-10)
REVERT: A  560 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8271 (mtpt)
REVERT: A  657 TRP cc_start: 0.6658 (OUTLIER) cc_final: 0.5148 (t60)
  outliers start: 17
  outliers final: 10
  residues processed: 101
  average time/residue: 0.0679
  time to fit residues: 10.3074
Evaluate side-chains
  82 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1034 THR
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1255 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 61 optimal weight:    0.2980
   chunk 28 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 943 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.126120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.102903 restraints weight = 9017.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 1.55
r_work: 0.2973 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7854  Z= 0.128
  Angle     :  0.619   9.434  10734  Z= 0.288
  Chirality :  0.041   0.267   1274
  Planarity :  0.004   0.032   1321
  Dihedral  :  8.780  76.384   1441
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.58 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.27), residues: 951
  helix:  0.64 (0.23), residues: 549
  sheet: -1.30 (0.60), residues: 63
  loop : -1.40 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 693 
 TYR   0.013   0.001   TYR A 646 
 PHE   0.020   0.001   PHE A1124 
 TRP   0.012   0.001   TRP A 960 
 HIS   0.004   0.001   HIS A 400 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7838)
  covalent geometry    : angle       0.58595 (10692)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       1.61288 (   12)
  hydrogen bonds       : bond        0.04180 (  412)
  hydrogen bonds       : angle       4.35393 ( 1188)
  link_BETA1-4         : bond        0.00758 (    3)
  link_BETA1-4         : angle       2.07412 (    9)
  link_NAG-ASN         : bond        0.00481 (    7)
  link_NAG-ASN         : angle       4.21888 (   21)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7561 (m100) cc_final: 0.7259 (m-10)
REVERT: A  560 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8253 (mtpt)
REVERT: A  616 MET cc_start: 0.8434 (ppp) cc_final: 0.7901 (ttt)
REVERT: A  657 TRP cc_start: 0.6509 (OUTLIER) cc_final: 0.5126 (t60)
  outliers start: 11
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0546
  time to fit residues: 7.7636
Evaluate side-chains
  83 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1047 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 59 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 722 GLN
A 926 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.127571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.103672 restraints weight = 9166.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 1.47
r_work: 0.2991 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7854  Z= 0.122
  Angle     :  0.570   9.483  10734  Z= 0.267
  Chirality :  0.040   0.291   1274
  Planarity :  0.003   0.032   1321
  Dihedral  :  7.997  70.555   1437
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.32 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.28), residues: 951
  helix:  0.86 (0.23), residues: 547
  sheet: -0.77 (0.62), residues: 64
  loop : -1.17 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 693 
 TYR   0.013   0.001   TYR A 646 
 PHE   0.022   0.001   PHE A1124 
 TRP   0.012   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A 400 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7838)
  covalent geometry    : angle       0.54813 (10692)
  SS BOND              : bond        0.00298 (    6)
  SS BOND              : angle       0.88582 (   12)
  hydrogen bonds       : bond        0.03894 (  412)
  hydrogen bonds       : angle       4.21181 ( 1188)
  link_BETA1-4         : bond        0.00656 (    3)
  link_BETA1-4         : angle       2.21833 (    9)
  link_NAG-ASN         : bond        0.00495 (    7)
  link_NAG-ASN         : angle       3.22798 (   21)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7580 (m100) cc_final: 0.7273 (m-10)
REVERT: A  616 MET cc_start: 0.8460 (ppp) cc_final: 0.8017 (ttt)
REVERT: A  626 ASN cc_start: 0.8547 (m110) cc_final: 0.8206 (m-40)
REVERT: A  657 TRP cc_start: 0.6372 (OUTLIER) cc_final: 0.4983 (t60)
REVERT: A  814 LYS cc_start: 0.4309 (mmtt) cc_final: 0.3657 (tptp)
REVERT: A 1203 GLU cc_start: 0.7680 (tt0) cc_final: 0.7445 (tt0)
  outliers start: 12
  outliers final: 10
  residues processed: 99
  average time/residue: 0.0648
  time to fit residues: 9.7357
Evaluate side-chains
  90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1034 THR
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0000
   chunk 16 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 339 GLN
A 507 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.126942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.103289 restraints weight = 9152.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.45
r_work: 0.2974 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7854  Z= 0.133
  Angle     :  0.578   9.499  10734  Z= 0.268
  Chirality :  0.040   0.291   1274
  Planarity :  0.004   0.040   1321
  Dihedral  :  7.648  65.945   1437
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.06 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.28), residues: 951
  helix:  0.93 (0.23), residues: 545
  sheet: -0.57 (0.62), residues: 64
  loop : -1.11 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 498 
 TYR   0.012   0.001   TYR A 646 
 PHE   0.021   0.001   PHE A1124 
 TRP   0.012   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A 842 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7838)
  covalent geometry    : angle       0.55281 (10692)
  SS BOND              : bond        0.00282 (    6)
  SS BOND              : angle       0.72033 (   12)
  hydrogen bonds       : bond        0.03903 (  412)
  hydrogen bonds       : angle       4.19921 ( 1188)
  link_BETA1-4         : bond        0.00595 (    3)
  link_BETA1-4         : angle       2.25480 (    9)
  link_NAG-ASN         : bond        0.00508 (    7)
  link_NAG-ASN         : angle       3.56943 (   21)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7585 (m100) cc_final: 0.7295 (m-10)
REVERT: A  534 ASP cc_start: 0.6788 (t0) cc_final: 0.6554 (t0)
REVERT: A  616 MET cc_start: 0.8453 (ppp) cc_final: 0.8057 (ttt)
REVERT: A  626 ASN cc_start: 0.8543 (m110) cc_final: 0.8222 (m-40)
REVERT: A  657 TRP cc_start: 0.6303 (OUTLIER) cc_final: 0.4881 (t60)
REVERT: A  788 MET cc_start: 0.8058 (mmp) cc_final: 0.7765 (mmp)
REVERT: A  814 LYS cc_start: 0.4433 (mmtt) cc_final: 0.3750 (tptp)
REVERT: A 1203 GLU cc_start: 0.7647 (tt0) cc_final: 0.7418 (tt0)
  outliers start: 14
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0538
  time to fit residues: 8.1969
Evaluate side-chains
  89 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1034 THR
Chi-restraints excluded: chain A residue 1047 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.126395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.102489 restraints weight = 9167.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.48
r_work: 0.2970 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7854  Z= 0.133
  Angle     :  0.582   9.560  10734  Z= 0.268
  Chirality :  0.040   0.287   1274
  Planarity :  0.003   0.031   1321
  Dihedral  :  7.384  60.388   1437
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.29 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.28), residues: 951
  helix:  0.96 (0.23), residues: 549
  sheet: -0.50 (0.60), residues: 74
  loop : -0.99 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 498 
 TYR   0.013   0.001   TYR A 646 
 PHE   0.022   0.001   PHE A1124 
 TRP   0.012   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A 842 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7838)
  covalent geometry    : angle       0.55012 (10692)
  SS BOND              : bond        0.00285 (    6)
  SS BOND              : angle       0.69954 (   12)
  hydrogen bonds       : bond        0.03863 (  412)
  hydrogen bonds       : angle       4.17206 ( 1188)
  link_BETA1-4         : bond        0.00478 (    3)
  link_BETA1-4         : angle       2.09406 (    9)
  link_NAG-ASN         : bond        0.00476 (    7)
  link_NAG-ASN         : angle       4.12066 (   21)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7594 (m100) cc_final: 0.7296 (m-10)
REVERT: A  607 MET cc_start: 0.8242 (mmm) cc_final: 0.7991 (mtp)
REVERT: A  616 MET cc_start: 0.8448 (ppp) cc_final: 0.7819 (ttt)
REVERT: A  626 ASN cc_start: 0.8540 (m110) cc_final: 0.8199 (m-40)
REVERT: A  657 TRP cc_start: 0.6209 (OUTLIER) cc_final: 0.4764 (t60)
REVERT: A  814 LYS cc_start: 0.4495 (mmtt) cc_final: 0.3889 (tptp)
REVERT: A 1009 HIS cc_start: 0.7427 (m170) cc_final: 0.7215 (m-70)
REVERT: A 1203 GLU cc_start: 0.7662 (tt0) cc_final: 0.7432 (tt0)
  outliers start: 11
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0533
  time to fit residues: 7.8844
Evaluate side-chains
  88 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1034 THR
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0000
   chunk 85 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.126879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.103868 restraints weight = 9141.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.42
r_work: 0.2966 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7854  Z= 0.144
  Angle     :  0.605  10.765  10734  Z= 0.277
  Chirality :  0.041   0.286   1274
  Planarity :  0.003   0.032   1321
  Dihedral  :  7.242  59.824   1436
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.29 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.28), residues: 951
  helix:  0.94 (0.23), residues: 548
  sheet: -0.38 (0.61), residues: 74
  loop : -0.95 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 693 
 TYR   0.013   0.001   TYR A 646 
 PHE   0.023   0.001   PHE A1124 
 TRP   0.011   0.001   TRP A 960 
 HIS   0.004   0.001   HIS A 842 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 7838)
  covalent geometry    : angle       0.56366 (10692)
  SS BOND              : bond        0.00311 (    6)
  SS BOND              : angle       0.73304 (   12)
  hydrogen bonds       : bond        0.03985 (  412)
  hydrogen bonds       : angle       4.18324 ( 1188)
  link_BETA1-4         : bond        0.00548 (    3)
  link_BETA1-4         : angle       2.05750 (    9)
  link_NAG-ASN         : bond        0.00460 (    7)
  link_NAG-ASN         : angle       4.80227 (   21)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7578 (m100) cc_final: 0.7279 (m-10)
REVERT: A  407 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8587 (p)
REVERT: A  616 MET cc_start: 0.8396 (ppp) cc_final: 0.7773 (ttt)
REVERT: A  626 ASN cc_start: 0.8492 (m110) cc_final: 0.8149 (m-40)
REVERT: A  657 TRP cc_start: 0.6081 (OUTLIER) cc_final: 0.4653 (t60)
REVERT: A  814 LYS cc_start: 0.4535 (mmtt) cc_final: 0.3972 (tptp)
REVERT: A 1203 GLU cc_start: 0.7649 (tt0) cc_final: 0.7412 (tt0)
  outliers start: 14
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0561
  time to fit residues: 7.9815
Evaluate side-chains
  89 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1034 THR
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 70 optimal weight:    0.0370
   chunk 43 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.6458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.127970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.105063 restraints weight = 9128.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.42
r_work: 0.2986 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7854  Z= 0.122
  Angle     :  0.575   9.591  10734  Z= 0.266
  Chirality :  0.040   0.283   1274
  Planarity :  0.003   0.031   1321
  Dihedral  :  7.062  59.956   1436
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.91 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.28), residues: 951
  helix:  1.05 (0.23), residues: 548
  sheet: -0.18 (0.63), residues: 74
  loop : -0.90 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 498 
 TYR   0.013   0.001   TYR A 646 
 PHE   0.023   0.001   PHE A1124 
 TRP   0.011   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A 842 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7838)
  covalent geometry    : angle       0.54581 (10692)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       0.64293 (   12)
  hydrogen bonds       : bond        0.03805 (  412)
  hydrogen bonds       : angle       4.11658 ( 1188)
  link_BETA1-4         : bond        0.00599 (    3)
  link_BETA1-4         : angle       1.64417 (    9)
  link_NAG-ASN         : bond        0.00458 (    7)
  link_NAG-ASN         : angle       4.01538 (   21)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7585 (m100) cc_final: 0.7285 (m-10)
REVERT: A  407 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8568 (p)
REVERT: A  607 MET cc_start: 0.8209 (mmm) cc_final: 0.7937 (mtp)
REVERT: A  616 MET cc_start: 0.8397 (ppp) cc_final: 0.7804 (ttt)
REVERT: A  626 ASN cc_start: 0.8520 (m110) cc_final: 0.8176 (m-40)
REVERT: A  657 TRP cc_start: 0.6059 (OUTLIER) cc_final: 0.4676 (t60)
REVERT: A  814 LYS cc_start: 0.4511 (mmtt) cc_final: 0.3988 (tptp)
REVERT: A 1208 MET cc_start: 0.8670 (tpp) cc_final: 0.8212 (tpt)
  outliers start: 11
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0545
  time to fit residues: 7.7789
Evaluate side-chains
  86 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1120 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.127093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.104263 restraints weight = 9080.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.41
r_work: 0.2982 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7854  Z= 0.134
  Angle     :  0.606  15.214  10734  Z= 0.276
  Chirality :  0.041   0.296   1274
  Planarity :  0.003   0.031   1321
  Dihedral  :  7.057  59.967   1436
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.41 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.28), residues: 951
  helix:  1.04 (0.22), residues: 548
  sheet: -0.11 (0.63), residues: 74
  loop : -0.89 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 498 
 TYR   0.013   0.001   TYR A 646 
 PHE   0.024   0.001   PHE A1124 
 TRP   0.011   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A 842 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7838)
  covalent geometry    : angle       0.55474 (10692)
  SS BOND              : bond        0.00284 (    6)
  SS BOND              : angle       0.67010 (   12)
  hydrogen bonds       : bond        0.03847 (  412)
  hydrogen bonds       : angle       4.12844 ( 1188)
  link_BETA1-4         : bond        0.00461 (    3)
  link_BETA1-4         : angle       1.89028 (    9)
  link_NAG-ASN         : bond        0.00436 (    7)
  link_NAG-ASN         : angle       5.41902 (   21)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7593 (m100) cc_final: 0.7283 (m-10)
REVERT: A  407 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8573 (p)
REVERT: A  607 MET cc_start: 0.8197 (mmm) cc_final: 0.7918 (mtp)
REVERT: A  616 MET cc_start: 0.8409 (ppp) cc_final: 0.7808 (ttt)
REVERT: A  626 ASN cc_start: 0.8512 (m110) cc_final: 0.8156 (m-40)
REVERT: A  657 TRP cc_start: 0.6071 (OUTLIER) cc_final: 0.4711 (t60)
REVERT: A  814 LYS cc_start: 0.4539 (mmtt) cc_final: 0.4003 (tptp)
REVERT: A 1104 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8380 (pt0)
REVERT: A 1208 MET cc_start: 0.8664 (tpp) cc_final: 0.8233 (tpt)
  outliers start: 16
  outliers final: 12
  residues processed: 94
  average time/residue: 0.0599
  time to fit residues: 8.5570
Evaluate side-chains
  90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  911 SER
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1034 THR
Chi-restraints excluded: chain A residue 1104 GLN
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 68 optimal weight:    0.2980
   chunk 81 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.127906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.105146 restraints weight = 9126.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 1.42
r_work: 0.2988 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7854  Z= 0.123
  Angle     :  0.615  18.861  10734  Z= 0.277
  Chirality :  0.041   0.356   1274
  Planarity :  0.003   0.031   1321
  Dihedral  :  7.111  59.800   1436
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.17 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.28), residues: 951
  helix:  1.11 (0.23), residues: 548
  sheet: -0.07 (0.63), residues: 74
  loop : -0.88 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 498 
 TYR   0.014   0.001   TYR A 646 
 PHE   0.024   0.001   PHE A1124 
 TRP   0.011   0.001   TRP A 960 
 HIS   0.004   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7838)
  covalent geometry    : angle       0.54959 (10692)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       0.62170 (   12)
  hydrogen bonds       : bond        0.03780 (  412)
  hydrogen bonds       : angle       4.11158 ( 1188)
  link_BETA1-4         : bond        0.00411 (    3)
  link_BETA1-4         : angle       1.75536 (    9)
  link_NAG-ASN         : bond        0.00438 (    7)
  link_NAG-ASN         : angle       6.16437 (   21)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.7599 (m100) cc_final: 0.7302 (m-10)
REVERT: A  407 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8560 (p)
REVERT: A  607 MET cc_start: 0.8125 (mmm) cc_final: 0.7887 (mtp)
REVERT: A  616 MET cc_start: 0.8399 (ppp) cc_final: 0.7824 (ttt)
REVERT: A  626 ASN cc_start: 0.8508 (m110) cc_final: 0.8178 (m-40)
REVERT: A  649 LEU cc_start: 0.7988 (pp) cc_final: 0.7755 (mt)
REVERT: A  657 TRP cc_start: 0.6006 (OUTLIER) cc_final: 0.4750 (t60)
REVERT: A  814 LYS cc_start: 0.4498 (mmtt) cc_final: 0.4087 (tptp)
REVERT: A 1104 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8370 (pt0)
REVERT: A 1208 MET cc_start: 0.8652 (tpp) cc_final: 0.8202 (tpt)
  outliers start: 15
  outliers final: 12
  residues processed: 92
  average time/residue: 0.0573
  time to fit residues: 8.4149
Evaluate side-chains
  93 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  657 TRP
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  911 SER
Chi-restraints excluded: chain A residue  966 CYS
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue  993 CYS
Chi-restraints excluded: chain A residue 1034 THR
Chi-restraints excluded: chain A residue 1104 GLN
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0030
   chunk 58 optimal weight:    5.9990
   chunk 60 optimal weight:    0.3980
   chunk 25 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.5790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.128230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.104717 restraints weight = 9066.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 1.47
r_work: 0.2993 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7854  Z= 0.116
  Angle     :  0.589  18.039  10734  Z= 0.270
  Chirality :  0.040   0.335   1274
  Planarity :  0.003   0.031   1321
  Dihedral  :  6.819  59.730   1436
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.29 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.28), residues: 951
  helix:  1.19 (0.22), residues: 549
  sheet:  0.02 (0.63), residues: 74
  loop : -0.82 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 659 
 TYR   0.013   0.001   TYR A 646 
 PHE   0.024   0.001   PHE A1124 
 TRP   0.011   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7838)
  covalent geometry    : angle       0.53513 (10692)
  SS BOND              : bond        0.00239 (    6)
  SS BOND              : angle       0.59625 (   12)
  hydrogen bonds       : bond        0.03695 (  412)
  hydrogen bonds       : angle       4.06504 ( 1188)
  link_BETA1-4         : bond        0.00744 (    3)
  link_BETA1-4         : angle       1.46280 (    9)
  link_NAG-ASN         : bond        0.00758 (    7)
  link_NAG-ASN         : angle       5.49118 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1840.05 seconds
wall clock time: 32 minutes 7.56 seconds (1927.56 seconds total)